How to Interpret Prophage/Host Ratio

[joshuakirsch]

Hi,

Thanks for making this tool! I'm a little curious as to how to correctly interpret the prophage/host ratio in the output file. In your opinion, would this value be valid to rely on? Or rather, should it be used to find active prophages? Can I use this value to compare the activation levels between two samples with the same prophage?

Thanks again!

[KrisKieft]

Interpretations can be different depending on the context of the samples. What I will say is that I don't think it would be accurate to use those values to provide "activation levels". Like if the ratio was higher in one samples vs another, I wouldn't say the phage was more vs less active. Many factors play into different ratios including complexity of the specific sample, sequencing depth, etc.